


Flying a Ship With Silver Lining

by Itar94



Series: Building Neutron Stars [1]
Category: Stargate Atlantis
Genre: Alien Culture, Alpha Rodney McKay, Alpha/Beta/Omega Dynamics, Angst, Building Neutron Stars: The John/Rodney Arc, Canonical Character Death, M/M, McShep - Freeform, Medical Drug Abuse, Omega John Sheppard, Pre-Slash, Season/Series 01, Slash, Wraith, alternative universe
Language: English
Status: Completed
Published: 2013-08-02
Updated: 2013-08-03
Packaged: 2017-12-22 04:49:37
Rating: Mature
Warnings: Graphic Depictions Of Violence
Chapters: 4
Words: 18,469
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/909110
Author URL: https://archiveofourown.org/users/Itar94/pseuds/Itar94
Summary: <blockquote class="userstuff">
              <p>It’s always been difficult, letting go of control. Even when in a galaxy far, far away, surrounded by life-sucking aliens, John hesitates. (All he has ever wanted to do is fly.)<br/>Meanwhile, Rodney struggles to figure out the puzzle that makes up Major John Sheppard and not get killed by aforementioned aliens or some other disaster in the process. (All he has ever wanted is to be acknowledged for being something more.)</p>
            </blockquote>





	1. Chapter 1

**Author's Note:**

> This is the first fic in a series set in a 'verse wherein Rodney McKay is both a brilliant scientist and an alpha, and John Sheppard is a reckless flyboy and omega. They struggle to overcome prejudices and each other, at the same time as they explore Pegasus and fight against Wraith. 
> 
> So, this is an AU, even if themes and episodes from the series are recognizable. If you aren't familiar with Alpha/Beta/Omega dynamics I suggest looking it up at Fanlore, though much in this 'verse is explained along the way. As always, I'm taking loads of liberties when writing and this fic is no exception. There is some angst but I don't think any trigger warnings are necessary, albeit some sensitive readers could be disturbed. This story involves a main omega character abusing/overusing (fictional) medical substances.

 

[ ](../../../tags/Building%20Neutron%20Stars:%20The%20John*s*Rodney%20Arc)

  
**Fl** **y** /flaɪ/  
[verb]  
 _to travel through the air;_  
 _be airborne; soar;_  
 _to use wings; be free_

* * *

In many ways, life is a bitch.

John can in all honestly say he knows this.

It’s just the way things are, he supposes, being the hotheaded, far-too-determined omega nobody really knows (people would turn eyes on him, wondering, seeking his smile, but he rarely gave away anything). Having practically lived on suppressants for the last fifteen years … helped. Sort of.

Deathly uncomfortable, perhaps, and painful and inconvenient from several sets of perspectives, but he can’t just walk around broadcasting the fact that, _yes,_ _I’m an omega, so what?_ in the world of stuck-up, powerful alphas and a couple of betas which make up the Air force (and any kind of military alongside it). Going into heat while in training or in the middle of an op really isn’t an option.

Between the choice of flying or being shipped off to be bonded to someone anonymous with more interest in his ass than his person, it wasn’t a difficult one to make.

His days at the Academy hadn’t been too bad. A bit lonesome maybe but that he expected, in fact welcomed. The pills helped making people think that he’s just an ordinary nondescript beta and effectively kept the alphas at bay – at a passable bay, at least, because he still got looked over and commented on for his good looks but that was it, no heat pheromones shaking off of him, no one pinning him down.

On the other hand it was totally okay for a beta to be odd and a bit geeky and not as outright macho as the alphas. Nobody believed he was that good at maths or physics or _thinking_ or anything really (except flying) until he was ordered to stand up and prove it, and John had nearly lost it then, not knowing whether to smirk and glow with pride at the fact that he finally was noticed even if it was just over an equation that he could solve with his knee-cap (in his sleep) or, if he should back down and refuse when realizing that he was standing in a room full of wide-eyed alphas, alone and unguarded and for the moment he wasn’t wearing a sidearm.

But no one figured it out then. And no one figures it out now either.

It’s somewhat of a shock to rise in the ranks to a Major – unheard of; an _omega_ , a fucking _Major_ (with a PhD that he tells few people about because it’s easier to slip by when they think he’s just another flyboy) – but inside he’s shaking and he can’t sleep when remembering Afghanistan and the curling smoke and the cries of dying men.

* * *

Antarctica is meant to be punishment but it’s a gust of fresh air and the cold, pale landscape is soothing to his soul. To soar above it is more calming than any medication.

Flying is being free. All he has ever wanted to do is fly.

* * *

The doctor – an omega, John senses, one not going on any medications or anything even if he’s standing in an underground military base (might be because it’s also filled with betas and scientists) – is going on and on about alien genes and transportations through the universe through wormholes when a hum tingles down John’s spine, urging him near the weird chair sitting on a pedestal and the doctor lunges out too late to stop him.

The hum intensifies – is it this ATA-gene thingy that the doc was on about, making him attuned with this ancient tech or is it something else? – and the Scottish doctor rushes out of the room. He’s back a minute later, a group of people in tow which John’s never met except the general whom he escorted here earlier, and the sharp scent of an aggravated alpha attacks his nostrils. He barely hears General O'Neill berating him for disobeying orders (again).

“Major,” says a voice; he glances slightly down and there’s an alpha in a bright orange fleece standing near his feet, and his pulse picks up at the closeness and this strange tugging somewhere in his chest. “Imagine where we are in the solar system.”

Then a galaxy forms above his head in blue and white lights, swirling and alive, and John wonders if he’s dreaming or just going crazy.

* * *

He packs lightly, taking only the necessary things. A Johnny Cash poster and a well-thumbed copy of _War and Peace_ (he’s going to finish it, one day, really, he is) and, hidden away where no one can find them, a stash of suppressant pills to last for at least a year (if he’s careful). It’s not a lot, but enough to get by, for now, and he has survived before. Having done this for year after year he knows how to slip it with him so that nobody notices – quantity is not an option.

It’s not going to be enough. If it is one-way and Earth will be a shadow behind them that they cannot reach, it definitely won’t be enough. But it’ll have to do.

(And in another galaxy, maybe, someday, he hopes, he won’t have the need to hide anymore. In Pegasus, maybe, someday, it won’t matter that he’s omega and still not mated, tied down. John has always feared being tied down.)

* * *

The Stargate is grand and breath-taking and startlingly simple. John hesitates to believe Lieutenant Ford’s admissions of it hurting to pass through the event horizon.

The unsteady blue dissolves as he steps through, and the world beyond is dark, until he takes a few steps in with that humming – just like with the chair back on Antarctica – at the back of his head. The city comes to life in lights and sounds. Dr Rodney McKay is half a step beside him and the scientist eagerly pushes past him following Dr Weir, their shoulders brushing ever-so-briefly and John halts sharply at the touch. Nobody notices, too occupied in exploring this new world – and, fuck, he’s in another _galaxy_.

* * *

The city is underwater and they’re running out of power already.

Figures.

“There’s no way to open a wormhole back to Earth,” Dr (Dr) Exasperating Know-It-All says sharply to Colonel Sumner, who isn’t too fond of Sheppard (the feeling’s mutual) and who  spent the last half hour barking orders at his men.

“What about somewhere in _this_ galaxy?” John suggests and calmly raises an eyebrow, meeting the startled, incredulous look McKay sends his way head-on. Has the man never been confronted with a thinking military man before?

Or maybe it’s just another of McKay’s traits, John figures, recalling seeing the alpha rushing about in the base in Colorado just before leaving Earth; the man had been fiddling with his laptop, running a dozen equations all at once and never giving it a moment’s rest, yelling at the other scientists in loud arguments, shouting at the lieutenants who knew no better than to cow beneath the heated gaze and generally bothering all and any other personnel available. John had given him a wide berth. But there was something, though. Like a tug at the bottom of his gut every time the man came into view. Almost like -

Not ready yet to face the implications, John turns to look at the screens filling up with data – shield collapse imminent, twenty-eight per cent of power left and dropping exponentially, radio static flickering in the background _–_ instead of the man’s face, as McKay thoughtfully nods.

“That’s relatively easy. We’ve already been able to access part of the city’s database and found some gate-addresses in storage.”

Weir nods, voice stern, without hesitation but John finds it difficult to miss the flashing in her eyes. She doesn’t want to evacuate. Not now. Not yet. It’s too soon, they’ve only just _arrived_ and already the dream is slipping away.

“Do it.”

* * *

“We do not trade with strangers.”

The woman – Teyla Emmagan – is tall and soft-looking, but John is pretty sure it’s a mask, one that could easily fool those without a sharper mind (those without their own secrets); there’s the underlying scent of an alpha, heady and firm, surrounding her albeit mixed with that of smoke and food cooked over fire in the tent. The villagers are tense and silent as they regard the earthlings and John doesn’t blame them. After all, how else could they react, but with distrust and suspicion, when a group of armed strangers appear in the middle of night?

They had stepped out of the gate expecting anything and yet been so unprepared, and John had been startled to find two children – alien, but human all the same – within aim of his P90. Then, a man had burst through the trees, pleading them not to shoot.

Colonel Sumner glares at him when he attempts to speak with the woman (honestly what’s the harm of mentioning Ferris Wheels? He’s just trying to break the ice), shooting the people his trademark grin, and John has to back down eventually alongside Ford. They leave the tent so that the colonel may sit down with the village’s leader and discuss a treaty. Outside the tent it’s cool and dark; he guesses it’s somewhere half-way through the night albeit John has no idea how long the days are on this planet.

The younger man’s jittery beneath the cool exterior, an anxiousness contradicting the arrogant certainty of his status as alpha rolling off him in waves. “I’m sure the colonel will, you know, break the ice with these people.”

“Yeah, sure,” John says (not as certain that Sumner’s attitude will be as welcome to the natives), glancing around. Now aware of their presence, the villagers have risen from their rest, tents lighting up from within, warm yellow glows from candles.

It’s starting to sink in now, that they’re in another galaxy on an unknown planet and millions of lightyears from home and they might never get back. He’s stuck here, surrounded by _aliens_ and military who glare at him ( _just another stupid beta who cannot follow orders, that one with the black mark)_ and a scientist in particular with an incredibly sharp, quick tongue.

And they’re _aliens_ , these people, even if they have human faces and human hands and – if they ever got a chance to medically test them – probably human DNA.

Atlantis was void of life when they arrived, but it somehow had felt more right to step into the city than it had felt to enter any home he’d ever lived in, any base he’d ever operated on.

They had woken the city only to break it – the shield collapsing slowly inwards, flooding pier after pier - and John wonders what the hell they should do if they really have to leave this place (though path of he knows it’s more of a question of _when_ , not _if_ ), where they’d go. For now, the only choice is this planet – whatever it was called – and its unfamiliar people, and they could only hope they will take pity and stretch out their hands willing to give aid.

* * *

Morning nearing, Teyla tells him about the Wraith, the great enemy (John briefly recalls the hologram Doctor Beckett lit up using his gene), and she speaks of cullings and human herds. John nods and replies calmly, but inside he might be freaking out because she’s basically stating there are life-sucking alien _vampires_ out there and they return every few hundred years or so to take their share. And these people have lived under their oppression of millennia, ever since the ancients packed up and left ten thousand years ago.

Teyla seems taken aback when she realizes that their world has never been culled, that it knows nothing of the Wraith and John vaguely lets it slip that he didn’t even know that there was anything like Stargates until a couple of weeks ago.

“And you are certain you cannot return home?”

 _Home_. Earth is home, he supposes, but he’s never really got the feeling.

He nods, shrugging. “We haven’t got the power.”

Sumner has already ordered Ford and a couple of the men back to the gate and they will return to Atlantis soon, empty-handed save for the news that there is a powerful, probably technologically advanced enemy out there somewhere set to kill all humans.

“Not all,” Teyla says softly when John voices the thought and she looks away for a moment, face darkened. “They always leave a certain number to reproduce. They cannot survive without food.”

John shivers.

“We believe,” she goes on, “that is why some are given gifts, so that we may mate and bear offspring to carry on the next generation.”

So that’s why she smells like alpha, why he’s spotted several couples emitting the clear scent of _mating_ and _lover_ in the main tent. Seems like humans in Pegasus aren’t that different, after all.

(Only here everything is much more dire and dangerous and _real_.)

* * *

By the time the fires have gone out and the smoke settled, fifteen bodies are strewn across the forest floor – villagers and marines and a broken, twisted anomaly which came down with the crashed alien craft – and many are missing, disappeared into the beams of light coming from the ships. People are crying and screaming and there’s nothing left but destroyed homes and ruined futures, and John cannot find Teyla nor his commanding officer anywhere.

Ford is the only one with the address to whatever the aliens – the Wraith – took these people.

When they return – the people are hesitant, not wanting to step through the gate at first when realizing that it would transport them to the ancestral city – there’s chaos in the gate room. Weir is shouting something. The scientists are rushing to and fro.

Now John ignores all this as he ushers the people inside, heart beating fast with adrenaline and shock – fuck, his men were just taken by freaking _aliens_. He steadies Jinto as the boy quietly asks if they can ever find his father again.

Weir rushes down then to meet them, yelling at them angrily but John meets her head-on, unlike what so many omegas would’ve done and he becomes aware of McKay approaching as well (hands full of data, eyes filled with purpose) when the city starts trembling.

Atlantis isn’t humming anymore in his head, it’s singing, as it breaks up through the ocean and into the sunlight. The shield no longer being under the heavy strain of holding back the water, the power consumption drops at once and McKay’s face is full of astonishment and glee as they receive the readings.

They’ve just received days and weeks, not the mere hours they had before.

In the exhilarating rush of _we’re alive, we made it, the city hasn’t crumbled down on us,_ John doesn’t put any distance between himself and the alpha as McKay joins him by one of the wide windows, an elbow pressed against his side, the man’s breaths tickling his neck.

Not until his pulse evens out and he realizes that McKay is staring at the curve of his ear. He takes a step away, flashing his trademark grin at the man, and for the first time he sees not the arrogant smirk but an honest smile of relief and happiness there, aimed at him. Maybe he’s an okay guy – if you oversee his petty attitude. Or his _whole_ attitude.

The pills mask his scent, but it’s been well over twenty-four hours since John took his last and McKay’s eyes narrow after a moment, like in suspicion; John doesn’t linger to give him more time to figure it out.

* * *

An hour later he flies the puddlejumper with his _mind_.

The great Wraith ship, which Teyla calls a hive, is eerily still and empty. There are oddly few guards, but John doesn’t realize why until later, when the Queen’s shrill screams have echoes across the planet and the Wraith begin to wake, one by one, small dots on the life-signs detector (another little piece of ancient tech that he found by just stretching out his mind just so …). When they find the captured villagers and marines, they are huddled in a cell, pale and shaken but all right. Colonel Sumner isn’t with them.

By the time John gets there, it’s too late, the man a living corpse attached to the Queen’s hand. It takes only one well-aimed shot.

Besides being life-sucking aliens, the Wraith are also somehow telepathic. It’s like she’s thrown a collar around his neck and is pulling him down, forcing him to kneel. She’s _furious_. John just barely manages to think _Fuck, Ford’s better get here soon!_ when she suddenly jerks her hand back, inches from his chest.

She’s got a bullet in her head and is still alive. Gunfire rings out from Ford’s hand. The grip on him lost, John rolls to the side and grabs the nearest object he can find, one of the aliens’ stun weapons and using it like a spear he guts her. That _has_ got to kill her.

“Sir! Sir, we got to get out of here.”

Ford rushes up to his side. Wraith are strewn across the room haphazardly and John glances at Sumner’s lifeless, unnaturally aged body as the Queen hitches a final breath, a smirk on her lips.

_The others will wake._

* * *

Upon returning, the surviving people of Athos rejoice in reuniting with their friends and family, and Jinto rushes into his father’s arms with a whoop; the people of Earth aren’t unaffected either, and there is celebrating. They have found what they have sought, the city of Atlantis, and it is tenfold grander than they had imagined – even if there are enemies out there, even if the Wraith have now awoken, even if the military commanding officer now is dead by a bullet John fired. Weir doesn’t blame him, but John knows how this’ll look in his records – even if he only worries for a while because this is Pegasus and they may never get back to Earth so then he has nothing to be concerned about.

Nothing to be concerned about.

* * *

There’s something about McKay that doesn’t make sense.

He is ruthlessly tactless with little thought of subtlety, so certain of himself and his theories, and he has an ego big enough to fill the whole of Atlantis and more. He’s selfish and greedy and generally the sort of person John wouldn’t imagine going on this mission, at first. Here there’ll be little chance of gaining fame or winning a Nobel, which he’s sure McKay wants – SGC is a secret and they may never return to Earth anyhow. McKay could’ve stayed there, been a brilliant scientist, found someone to mate with – John has found no evidence yet that the man was mated but maybe there’s someone back on Earth – because even if his personality was lacking, he was still an alpha and when in heat an omega would be willing.

(That’s what’s frightening to think and John fears what’ll happen once he runs out of medicines and he is forced into heat. Will he be respected, the alphas keeping their distance, or will the inevitable finally happen …?)

Still, McKay chose to come here, to Pegasus, risking his life merely by stepping through the gate. He doesn’t seem like the person to sacrifice for others and this expedition is very much a collective experiment, wherein everyone must think not just about themselves but about others.

McKay looked at him sometimes, with clear blue eyes, like he was ready to devour him and it gave him goose bumps all-over for some reason. People have looked like that at him before; he’s not unused to people complimenting his looks, a hand reaching out to clasp his arm, touch his back but he’s always shied away.

John doesn’t like being touched. Having people stand too close. Other omegas were okay, like Doctor Beckett, and some of the scientists, but he wasn’t sure how to act now when surrounded by some many betas. And there are so many alphas as well, not just the marines but some of the civilians, chosen for their brilliant minds and not their bodies.

It’s not like they’re keeping tabs but over the days, he’s figured out at least eight other omegas on the base, both male and female – and they don’t hide, because they aren’t in the military and don’t fear. Nobody raises an eyebrow at omega scientists or doctors; in fact it’s perfectly natural and expected. The alpha scientists are a bit more unexpected. Several of them aren’t particularly buff or loud or anything else that one directly connects with alpha behaviour.

Maybe, John ponders, it’s because he’s been around military for so long it’s strange not to hear the scientists make those laidback comments about _claiming_ and _taking_ and _breeding_ – words he’s never liked, his gut curling in unease, but he’s always smirked alongside them nonetheless. (They never talk about _giving_ or _sharing_.)

The scientists don’t act like that. Perhaps it is unnecessary for them. They compete amongst themselves in other means, and right now everyone is just busy trying to save the city and everybody in it to care about competition and showing themselves as strong alphas right now.

* * *

There’s a dark, shapeless monster on the loose slowly emptying their power generators.

By the time he finds Jinto, Halling’s son, huddled in the corner of a storage room, the thing has been loose for several hours. McKay is there too, searching for the boy with him, a datapad resting in the scientist’s hands and he’s staring at it intently, reading some sort of power output or another. McKay has been riding on some sort of high all since he got his gene therapy and found an ancient personal shield, making him essentially invulnerable since four hours back. Halling’s wounded leg stopped him from joining them in the search for the missing boy.

John listens to him with half an ear as suddenly Jinto leaps out of the shadows and into his arms without concern for the weapons John is wearing. “Major Sheppard!”

“Jinto!” Kneeling to be at the boy’s level, John takes in his appearance. He looks shaken but unhurt. “You okay, buddy?”

“Hmm,” McKay says, approaching some orange device, its shape a vague resemblance to their own naquada generators, sitting on a console in the middle of the room. There’s intent written all over his face and John finds his gaze inexplicably drawn to his fast-working hands, pressing buttons at an impressive rate with a weird sort of elegance. Before he can delve more into the matter, John averts his gaze, focusing on Jinto instead. He suspects the boy may be hero worshipping him since he and his team of marines rescued Halling and Teyla and the others from the Wraith.

“This could be some sort of research lab. Not the first we’ve come across. These consoles generally access the central computer systems, so Jinto could have caused what we thought were malfunctions from here.” The scientist pauses and John drags himself up, Jinto’s gaze flickering nervously between the two men as McKay looks at the boy sharply. “Look, I need to know _everything_ you touched.”

* * *

It takes a while to track down the entity and figure out what to do with it. It’s dangerously close to disaster when they do.

Once it’s finally gone through the gate, thanks to McKay’s spur-of-the-moment decision to wear the shield he’d struggled (and fainted from manly hunger) to get off, everyone exhales as one and they can relax, at least for a moment.

There’s still the Wraith and who knows what else out there to worry about, and the majority of the city is still unexplored; anything could be hiding in the long corridors and abandoned rooms, like that energy-sucking entity. But for now, everything is okay, they’re alive and well, and John can get a proper night’s sleep for the first time in two weeks.

McKay’s actions have raised John’s opinions of the man some. The man basically saved their asses in a stroke of reckless selflessness. So maybe he isn’t that much of a git, after all.

* * *

When Weir tells him to organize a gate team for off-world exploration, insisting on a scientist on it, John decides fairly quickly. Besides being decidedly smart and sharing (some of, at least) his wit, the man has proven himself to be someone they can depend on in dire situations, and he’s also the only scientist John really knows. There’s this Kavanagh guy whose John’s only experience with was when the pony-tailed man made a rude off-hand comment, so, not really an option, and while Dr Zelenka seems an okay guy he’s just not made for fieldwork.

McKay is also one of the few alphas that John feels comfortable enough around to jibe and joke with, even if the man sometimes gets a bit too close, stepping into his personal space without boundaries, not seemingly able to read simple social codes like _Please step back you’re standing too close to me_.

(Choosing him to be on his team has nothing to do with … with whatever he might be feeling whenever McKay enters his vision.)

He also chooses Ford, because the young man’s a good solider and John trusts him to have his back and then Teyla, because she has requested to help them and she’s mild-mannered, good at negotiation and talking and at the same time a good fighter (he’s seen her work out in the gym once beating the hell out of a marine using a pair of wooden sticks). He can trust her.

Trust is difficult to come by and keep. Trust is, for him, difficult to take to heart and not simply push away but he’s a soldier and he’s learned to trust comrades in battle, just like he’s learned to take aim and pull the trigger.

When facing McKay about the decision, the scientist merely shrugs, busily running a simulation on his computer and he waves a hand nonchalantly in John’s direction. The space which the alpha has occupied as his private lab is propped with computers and machinery and the room has already begun picking up McKay’s scent. Being in there makes something in John’s mind reel.

“Well … okay,” McKay says, sounding not too enthusiastic about the prospect of having to start carrying a sidearm; “As long as you guarantee that I won’t be shot down or mutilated or die in some other horrible way at once, flyboy and, oh, I _will_ have time for research and _science_ , right?”

Which sounds fair enough. You know, when you’re stuck in a galaxy far, far away filled with life-sucking aliens and ten thousand year old sunken cities.

* * *

John’s body is slowly numbing away. The pain, at first sharp like a knife working its way through his veins, ebbs away and then he realizes he cannot move his legs, cannot lift his arms, barely move his head as it is, as the bug digs into his neck harshly.

They’re lodged half-way in the gate with thirty-eight minutes left until the ship will definitely split in two.

 _McKay, come on, you can fix this,_ John thinks, a mantra he holds onto as the world begins to blacken around the edges; _I’m counting on you._

As he’d come to after the crashing halt, McKay had kneeled by his side, a hand on his shoulder – the one without the bug resting on it – and having his hand there had been comforting, steadying him. When McKay had removed it to stand and work on a crystal panel, John already missed the warm grip.

The minutes trickle by and, afterwards, his memory is fuzzy of the whole ordeal. He remembers pain, abruptly sharp and he might have screamed, sound ripping out of lungs and then, he’d ordered Ford to use the defibrillator, holding his stare and McKay had looked on disbelievingly, John glaring at him to _Keep working, fix it, McKay!_ and there was a white soaring flash of memory and then –

* * *

He wakes in the infirmary, hours later, a terrible bruise on his neck and his body sore but otherwise unharmed.

McKay had fixed the jumper, retracting the pods just in time and then Ford had saved them all by blowing open the rear hatch, getting the jumper through the gate. Pride swells in John’s chest when he hears the report, as they stand around his bed; his team and Weir but most importantly McKay, who’s looking at him with such warm intensity like he cannot quite believe he’s there and for once John doesn’t mind. (He can’t quite believe he’s there either.)

He’s never liked infirmaries or hospitals. Not because of the whiteness, the smell of medicines and the doctors swarming around, too many hands and eyes and ears. But a doctor could always figure it out; a simple blood test would reveal the chemicals from the pills and a full exam could always conclude in his secrets being leaked. And then …

He wonders if Carson knows.

His team isn’t looking at him any different now, as they stand around him; Teyla is calm, as always, collected and firm whereas McKay is a bundle of energy. Ford is on another bed, asleep; having been briefly exposed to vacuum isn’t good for anyone. As they take their goodbyes and leave him to rest, John is aware of McKay glancing back at him, but no more words are exchanged.

Then, Carson approaches his bedside. “I believe we need to have a word, Major.”

John doesn’t swear aloud but he does in his head, and he may look calm on the outside but his gut ties itself into knots. _No. Don’t let anyone know, please. Don’t let them have me degraded, don’t let them send me away to be mated –_

“I found traces of heat suppressants in your blood system.”

“… Yeah.”

“You _are_ aware that they are not originally meant for long-time consumption?”

John winces. He knows. There are warnings on the packets, fierce letters in red, and he knows because he’s experienced the pain and nausea of long-term use, when he has forced his heat away for months and years at a time, his cycle wholly disrupted and his body crying in pain.

“Yeah, doc. I know.”

The man sighs and shakes his head, muttering something about stubborn military and John weakly cracks a smile. “Look, doc, I just …”

“I know that the military aren’t too fond of omegas in their ranks, Major,” Carson cuts in, gently, “so I do understand at least some of your reasons to taking them. But from what I concluded from the tests you’ve been eating suppressants for a dangerously long time, possibly several months. There are side-effects, and your body must be given time to work in its own pace as well. When was the last time you entered and went through a natural heat?”

“Uhm,” John looks away, at his hands, suddenly embarrassed because it’s been _years_ and it’s not normal, he’s over thirty years old for god’s sake and – “Five years ago, give or take?”

(He’d been on leave for four weeks, back in the States after long months in the unforgiving dry desert. He’d thought it’d be well more than enough, but after locking himself up in his basement for those long awful days, body aching and trembling with need, alone and cold in the dark, he’d felt hollow and empty when letting himself out again. It’d fucking _hurt_ and he hated being so alone but there were no other options and two weeks later, just as he’d begun recovering, he’d been sent back out to the front again, dust on his jacket.)

The startled look on the man’s face indicates that this is probably very, very bad. “Lad –”

“Look, doc, I know it’s not … _ideal_ , but –”

“I’m just saying, major, that you should give your body some rest by allowing it to go through a heat or two. Postponing it for this long can be potentially very harmful.”

He can’t. Not now. (Then _when_?) “I am not going through heat now, doc. I _can’t_.”

The doctor sends him a helpless look. But, there’s some understanding there too. And when John insists, Carson finally nods and he says, “As long as you’re certain, lad.”

He isn’t, but he has no other choice, he can’t face questions right now and definitely not a mating. He’s not ready for that, or willing.

“This is confidential, right?”

The man looks for a moment like he doesn’t want to agree, but eventually nods jerkily, knotting his hands against his crisp white coat. “It is. Unless you are having suicidal thoughts?”

“What? _No_. No. Nothing like that, doc.”

It could be worse.

It could always be worse (he tells himself and holds his breath).

* * *

There’s something about John Sheppard that doesn’t make sense.

To Dr Rodney McKay, PhD, PhD (most brilliant scientist in one, probably two, galaxies), this is especially frustrating. To not be able to pinpoint or calculate a problem is direr and more nerve-wracking than meeting with alien cultures or avoiding a planet-wide attack and saving millions of lives in the process. No. He’d face any improbable equation before this one.

There’s something about Sheppard that just cannot be solved.

The man is laidback and he smiles often to a whole lot of people and Rodney could easily overlook him, except he’s hinted that he’s actually got a brain between those ridiculously pointy ears and the man is fucking _gorgeous_ , even if his hair hasn’t seen a comb in years.

Rodney wouldn’t mind having him in his bed, no, not at all, but Rodney has never been good at this relationship thing and despite the man being a typical flyboy there’s just _something_ … something that Rodney doesn’t want to ruin with a one-night stand. He wasn’t really good at one-night stands either to be honest. He’s far too possessive for that. Once he’s got his hold on something, he wants to keep it that way, only it’s difficult to balance people with science, with time.

Maybe that’s why he’s never settled down. Never let his heart be captured, as cliché and stupid as that sounds. Oh, fair enough, he’s lusted after his fair share of men and women and for a while – which was an awkward time no one is allowed to mention – he had the hots for Samantha Carter, even if they were entirely incompatible (even if she’s quite smart). No alpha would be able to stand him. The only upside of an alpha-alpha relationship would be the lack of kids – he’s never liked them that much anyway, they’re only in the way. There are few children he's tolerated for more than ten minutes before he wants the mout of his sight and hearing range.

Which brings him back to the puzzle of Major John Sheppard. A fairly good pilot but he’s got a black mark in Afghanistan (getting a hold on his file wasn’t difficult. Rodney read it out of curiosity, nothing more, between working hours back at SGC). Kind of clever, for a military man anyway. Easy on the eyes, with a warm drawling voice and hazel eyes. Not to mention he has the gene – okay, so Rodney's a _bit_ jealous that this man had the strongest naturally occurring gene they’ve ever come across.

His scent … it’s _addled_. Almost non-existent - which is the case of all betas.

It’s kind of a pity … because if Sheppard was an omega (even an unruly, rule-breaking, stubborn omega), at least Rodney would have a legible, unquestionable excuse for wanting him.

But now, with Sheppard being beta, why would he ever want to lie down and spread his legs for Rodney? There’s no reason. He can’t even be sure that Sheppard’s gay (even if his hair is a bit too wild for a straight military guy) and even less know if the guy is interested in him in any manner.

* * *

He doesn’t want to accuse anyone of being a spy and neither does Weir or nearly anyone on the base.

But McKay was just shot with a Wraith stunner right in the face and the moment he fell, there in the gate room, still and silent onto the floor - John’s heart had stopped for a moment.

Then Sargerant Bates, who oozes with confidence born out of the fact that he’s alpha and military and has the upper hand, has the guts to accuse _Teyla_ of handing off information to the Wraith and John gets rightfully pissed in addition to worried. Clearly Bates is a blind idiot because Teyla’s people were driven from their home planet by the Wraith, her people have been killed by those creatures generation after generation and she’s grown up under their shadow. Anyone having met her should have seen the fire in her eyes as she spoke of the Wraith and know that she _never_ would betray any other human to them.

* * *

While Rodney recovers – fairly quickly, even if he complains about his numb foot for hours after he’s let out of the infirmary – investigations starts and the Athosians are confined to their quarters as they are taken out for questioning, one by one. John feels a little sick thinking about it. These people couldn’t – _surely_ …

“This is stupid.”

John glances at the scientist who takes another sip of his coffee, eyes fixed on the screen.

He’s not sure why he does it, visiting Rodney in his lab now and then, just dropping by. Between missions and meeting in the mess hall, this is where they see each other. At least, despite calling him a flyboy, Rodney tolerates his presence. Plus he probably wants him near to light up ancient things with his gene – and while it’s not ideal (nothing is ideal) it is enough for John.

He can’t recall the exact moment when he became Rodney instead of McKay.

“Which one, those equations you’re looking at or the questioning of the Athosians?”

“Well both. One can _obviously_ see the blatant errors in this theory, at least if you have an IQ higher than a peanut, which _completely_ disregards the existence of –”

John rolls his eyes and smirks and quietly admits that Rodney can be kind of cute.

Well, for an alpha with attitude problems.

“- and anyhow,” Rodney’s saying as John bites his tongue and returns to the world, heart thundering, “if there were spies in Atlantis why haven’t they attacked the city yet? It’s illogical, unless of course they’re taking their time in coordinating an attack in which case I’d say we’re well and very screwed – oh, look, you! Czech guy!”

Rodney clicks his fingers to get the attention of the scientist who just entered the lab, one whom Rodney clearly can never recall the name of but John recognizes him as Dr Radek Zelenka. The man has this nervous look about him, brown hair falling into his eyes as he keeps readjusting his glasses, pushing them further up his nose every fifteen minutes. Another of the omega scientists that no one raises an eyebrow at.

Well, fair enough, all known omegas get checked out by the alphas every now and then, especially when signs come telling that they’re nearing heat. It’s a distraction for the marines, having all of these omegas on the base, but it keeps their minds off the impending threat of life-sucking aliens for a while. If only they’d stop leering and _staring_. John doesn’t know how to tell his men to stop doing that without raising too many eyebrows.

(Maybe had he pursued a scientific career John wouldn’t have bothered to hide as he does now. He could have become an engineer or mathematician or whatever, but he could never have gone through with it if it meant never being able to fly.)

“You know who wrote this?” Rodney asks Radek furiously, gesturing at the whiteboard. And all focus is back on the stupid backwards theory again. “This is idiotic! This variable here …”

* * *

John wonders if Teyla’s all right, if her people are coping well under the pressure of being accused of being spies in the city that took them in as refuges. Guilt tugs in his belly. If they hadn’t come, if they hadn’t been caught, if he hadn’t killed that Wraith Queen then the others wouldn’t have woken and they wouldn’t be in this mess.

If they hadn’t come through the Stargate, if he hadn’t flown to Antarctica and met Rodney –

He bites his tongue again; _don’t go there now._

(Don’t go there ever.)

* * *

Finally they come to realize that the spy was not a person, or even a sentient being, but an innocent looking necklace that had caught John’s gaze as it had gleamed between the sand back on Athos. Unknowingly activated at his touch, for all these weeks the Wraith had become aware of them – of some people out there carrying the Ancient gene.

Again, the guilt comes creeping up on him but at last there’s something they can do about it. The trap is set and they don’t have to wait long for the Wraith to show up; three drones and another, taller one without a mask. They take down two quickly and then move to capture the third alive, but its self-destruct activates before they can act. John barely manages to yell “Take cover!” and the marines on the oppose side of him turn around.

The ground shakes by the explosion and John and Rodney are thrown back, tumbling down a slight slope until they come to a halt between some jagged rocks – the last remnants of some long ago fallen civilization. John’s ears ring from the explosion, dust and adrenaline lingering.

He rolls over onto his back, glancing at the alpha, who’s got a small gash on his forehead but otherwise looks fine. “You okay?”

“Yeah, yeah, fine,” Rodney groans, rubbing at his neck, “nothing broken. I think. Gods, what was that? I didn’t know Wraith could self-destruct. Ugh, my ears are ringing.”

“Didn’t know that either.” He comes to his feet and tugs on Rodney’s arm, trying not to think too much or else he’ll never stop dreaming about touches. “Come on. There’s still one of them left.”

* * *

Teyla heads back to the mainland shortly thereafter, to where her people have been relocated. They are more at ease there, she assures him when John asks if they’d not rather stay with them in the city. Some of them still fear Atlantis, the city of the ancestors, and they are more comfortable near the woods under the open sky. They can grow their own food there, as well, and the children won’t be in the way.

John doesn’t tell her or anyone out loud but he’ll kind of miss the laughter of the kids and having them running down the corridors – it had kept him at ease. But he understands. Atlantis isn’t that safe; it is a military base more than anything else, despite the majority of civilians. It’s a war zone, the Wraith still out there, hunting for them.

* * *

There’s still a Wraith in one of the cells at the bottom of the city left to deal with, trapped between the bars. It does not pace. It just stands there, still, with a confident patience born out of a life hundreds of years old.

John goes down there alone this time.

“Again?”

The edges of the Wraith’s voice are jagged with dry humour and had it had any eyebrows John is sure they would’ve raised one of them.

“Your kind is persistent. I thought you would have given up by now.”

“I got all the time in the world. You, on the other hand …”

There’s already hunger in its eyes, furious and raw and it slams a hand against the bars, toward John’s chest, drawing back only as it is stopped by a blue force field.

“I’d give you a week, maybe two, tops …” Taunting it is only so effective.

“You waste your time, human. I will provide you with no information.”

“I wonder what hurts more,” John goes on as if he hasn’t heard. “The gunshot wound or the hunger. I’d love to help out, but, how’d McKay put it? ‘We can’t meet your dietary requirements.’”

“You may think,” the Wraith hisses, “that by my capture, you have won a victory. But by bringing me here you have only hastened your own doom.”

And somehow John’s got a feeling it’s not just an empty threat.


	2. Chapter 2

The children are still aiming their Stone Age bows and arrows at them, feral wild looks on their faces and Rodney just won’t _shut up_. John elbows him again. Now’s not the time. Even those homemade backwards weapons could be harmful even potentially deadly if aimed at the right spot, and he doesn’t fancy having any of his team killed by these children.

There’s no one older than twenty-five in the village, as far as John can see. Not a speck of greyed hair. The children confirm as much, speaking of afterlife and sacrifice and peace for five hundred years – not a culling for generations. And as realization starts to dawn on them he feels a bit sick. He hides it better than Rodney though, who looks utterly disturbed at the notion.

“It’s crazy. _They’re_ crazy -”

John hushes him before the tirade can even begin.

They have no medicines of any kind other than what they’ve come up with using local plants and wildlife, and their homes are simple, hidden up in the trees (reminding John of the ewoks in _Return of the Jedi_ ). They hunt instead of farm. It’s children taking care of children, having no idea that they have no _need_ to kill themselves because age doesn’t matter to Wraith, they would have come anyway if not for the magnetic shielding around the place. But explaining this is difficult when they have never heard of electricity, never mind ZPMs.

They’re so young and lost and John wonders how the hell they started this…this _mess_. Who the fuck managed to convince them it was the right way? How? _Why_?

* * *

One of the elders, as they’re called, is twenty-four year old Keras, apparent leader of the village. Just a year younger than Ford – John hasn’t realized until now how young Ford is, really; and thinking about himself then, thirty-four, alone and unmated, makes him reel.

Keras is alpha, scent unmasked, and in his hut there’s an omega, female, introduced as his mate. She’s heavily pregnant and doesn’t look a day older than sixteen. And there’s another, a male omega, younger than twenty-four evidently but older than the girl and he walks up to Keras, laying a hand on his shoulder. “They’re trespassers. We don’t have to explain ourselves.” As a ray of sunlight falls from a window of the tree-hut, falling onto the pair, it becomes evident that he is pregnant too.

Like a last struggle for survival, they breed while they kill themselves.

Teyla is most likely to bring sense to them, so John lets her do the talking while Rodney itches to investigate the strange energy signatures he’s been reading for the past hour.

“There is a shield around your villages, around a designated area,” she tries to explain. “It matters not how old you are, as long as you live within the shield. As long as you stay within its boundaries you can live full lives without fear.”

But they don’t understand, merely proud to announce that their sacrifices are necessary for the survival of their people.

* * *

Rodney finds a ZPM hidden under the shadows of an old tree, effectively being able to shut the field off so that they can leave. But John is torn.

Keras will kill himself tonight. There’ll be no more years ahead of him but he seems set stern, proud even, to protect his people this way and he smiles a little as he says he’s leaving offspring behind, letting life of his people carry on.

John feels ready to burst in the seams, barely controlling his frustration as he stands in the centre of one of the twelve villages.

“You could live a full life. Your people won’t be more or less protected if you choose not to—”

Because John can’t just walk away and let this young man _kill himself._

Keras steps up to him then, collected and calm. “You are a warrior among your people, are you not - one who is trained to defend and protect them? Would you not willingly lay down your life when necessary, as to ensure the survival of the next generation?”

“There is another solution,” John says.

Unfortunately, Keras refuses to listen until nightfall is close, when the ceremony has just begun and John realizes that there’s a Wraith device blinking in the centre of the village, broadcasting their location to the rest of the galaxy and alerting the Wraith of the humans’ presence.

* * *

Carson calls him back for a talk shortly after they return from M7G-677. Well, records will probably state a general physical examination or something likewise vague and fit for protocol, but John goes simply because otherwise the doctor wouldn’t stop pestering him about it. They are alone in the room. John didn’t bring a radio.

“Have you given thought to my suggestion, Major, about giving medications a rest?”

He finds an interesting pattern on the floor. “A little, doc. Maybe.”

“It’s been nearly three months now, and in addition to the time before we arrived here –”

John glances at him, hearing the steel slipping into the doc’s tone. “I need time, doc. And solitude. That’s hard to come by here, I think.”

“You don’t have to be alone,” Carson says softly with a small sigh as John merely squares his shoulders and averts his gaze again. “There are people on this base who you can trust, who would help you if you allow them.”

The thing he recalls mostly about his last heat is the pain, at first, and the burning _need_ eating him up from the inside day after day, night after night, brutal and unforgiving, and the vulnerability of his own body and soul.

“I’m not sure I could trust anyone,” he admits quietly. “Not when I’m … Not then.” Because _who?_

Rodney. No. Not Rodney. Rodney’s an alpha. It would only lead to … No.

“I could request a leave for you, pull a few strings.”

They have no way back to Earth yet, so that’s obviously out of the question. And there is no viable friendly planet to go to; perhaps somewhere uninhabited, but how could anyone motivate that without slipping the truth in? God, John doesn’t know if he’s ready to let everybody in on the truth.

“Perhaps you could stay on the mainland for a week or so?”

John doesn’t reply, only shrugs, looking at the doctor for a moment and Carson sigh quietly in defeat as the major leaves the room.

* * *

“What’s up?”

“Huh?”

Rodney settles in front of him in the mess hall, plates and glass rattling and John looks up, surprised. He thought Rodney was too busy with some experiment or another to pass by just for a chat; well, there’s food, so that explain some of it.

“You’re acting off. Weird. So. Look, Sheppard, I’m not good at this talking business, let’s be honest, but you if there’s anything –”

It’s an oddly sweet gesture but also awfully awkward and nothing’s wrong, at least not in the manner that Rodney might think, and John just doesn’t know how to speak up about it. How to explain to his friend – he’s pretty sure they _are_ friends, by now – that despite those stupid pills he can’t calm down his quickening pulse every time he sees Rodney, every time he hears his voice over the radio, can’t keep away the dreams at night wherein Rodney …

“Everything’s fine.”

(It is. From one perspective or another.)

* * *

Everything goes haywire then. The Hoffan drug, trickling into the blood of hundreds of innocent and strangling them to death; it kills the Wraith, but also the human carrying it, and the leaders of the Hoffans are blind in their hubris that this is right, this will work, this _immunity_.

Every time he passes through the gate along with more medicines and supplies for Beckett’s team offworld, John steels himself for the sight of more lifeless bodies, more ill people struggling to survive, and the fear of it being someone he knows.

Eventually, they can do no more. The people vote - ninety-six per cent in favour for spreading the drug. For slowly killing themselves.

They won’t return to the planet for a long time.

* * *

John had to agree with Rodney that it would be so much simpler and less dangerous if people could just keep their secret underground hatches locked.

Instead they find themselves at gunpoint, deep inside a bunker wherein the Genii are trying to build a freaking _atomic bomb_. John really, really doesn’t need Rodney’s endless babble about radiation level dangers and physical advancement improbabilities right now.

The debate is rather frank and short but that is the way John prefers it. It helps, a little, when Ford and Teyla are taken down as well, unarmed but uninjured, because Teyla speaks well for them but it would have been easier if the two had been able to escape to the gate and call for backup. Now they have little choice but to deal with these people, agreeing to their terms unless they are to be shot in the head and reported taken by the Wraith.

“Seriously, five years? There’s no way they’d be able test that weapon in five years. Fifty’s more like it. Except they don’t have fifty or five years with the Wraith all woken up now and all.”

“Rodney –”

“I mean seriously. Have you had a good look around this bunker, major? We’re at least sixty years ahead of these guys and still the -”

“ _McKay_. Shut up.” After appropriately elbowing the scientist John flashes a pleasant smile at Cowen, leader of the Genii. “The important thing is, are we discussing this as allies or are we still prisoners?”

* * *

They raise toasts of foreign wine (at least Pegasus version of wine) for a new albeit shaky alliance and twenty-four hours later, a puddlejumper enters the gate, loaded with C4 and the goal to steal a data device possibly carrying the intel they might need to take the Wraith down.

* * *

Still recalling the shrill alarms ringing across the whole hive, they return to Atlantis with darkened faces, having lost this recently gained ally and their nukes – not that it would have made so much difference, they realize when browsing the data of the stolen Wraith data device.

Over twenty hives in this quadrant of Pegasus alone. How many are there in total? How long will it take to take them all down?

They have no other means to get more supplies and food other than through allies. The list remains thin and fragile.

* * *

Afterwards, when he’s showered and rested for a bit, John is pleasantly surprised to find Rodney in the mess hall, a sandwich in one hand and a datapad in the other. A full plate of food is waiting for to be devoured, yet Rodney is fully focused on the data flashing by his eyes. It’s a grand feat for Rodney to be distracted from food and John smirks at the image.

Sneaking up on an alpha is usually quite difficult, their senses on high-alert, any scent able to put off their balance if strong enough. But having just taken another pill, John’s scent has been subdued into nothingness once again and seeing the scientist jump makes him chuckle evilly.

“Are you _trying_ to give me a heart attack?!”

The scientist grumbles something about stupid flyboys with no respect for brilliance as John takes seat, the omega eyeing the plate across the table and stealing some of the fries (well it’s not really fries, not made of potatoes but something that the Athosians have grown on the mainland, similar in texture).

“Watcha doing?”

Rodney types in something. “Determining exactly how many hives are waiting out there to bear down on us like starving people would attack a smörgåsbord.”

“You should take a break.” John means it.

“A break, what, _now?_ No, no, this is far more important and – hey! Those are my fries!”

“I don’t see you eating them.”

He grins. Nothing quite matches the feeling of riling up his favourite scientist.

* * *

As the fog fades and they step through the gate, there’s something off, John can _sense_ it.

SGC is oddly stilted and pale but then, he wasn’t here for that long before going to Pegasus so he could be wrong. All faces are unfamiliar save for the brief flashes of General Hammond, whom John hasn’t spoken to before and they exchange just a few words. It’s … _strange_ when he’s redirected from his quarters on the base to a bachelor pad further south, Teyla coming with him to discover the Earth once clearance has been given and then all of these people he has vague memories of begin to show up. Ford is there too, in a corner, laughing with some men John hasn't seen for countless years. But there is no sign of Rodney.

Maybe it is one of the factors tipping him off that something is terribly, terribly _wrong_ here. Not that Rodney would enjoy (he thinks) a beer with them right now, rather the scientist is probably busy with some experiments or whatever back at SGC, but his lack of being there – there hasn’t been a word, not even a call – is unsettling, creating this hollowness inside John’s chest.

He’s not sure who dug it.

The scale tips wholly though when he’s greeted by the faces of comrades-in-arms long gone, their eyes alive now, bright in the sun and their voices rich and real. He’s never allowed himself to be too close to anyone, never let them touch, but suddenly shoulders are bumping with his and the musk of alpha invades his senses. And this longing, deep and wide etched into his spine starts spinning out of control; he wants to be touched, wants to left alone, wants Rodney to be there, it’s all paradoxes - and it’s wrong, all _wrong_ and then he finds a gun lying on the living room table.

The next moment, the illusion shatters into another, the Stargate quiet and empty behind them. Rodney’s there, _finally_ , looking just as confused and startled as him, as General Hammond speaks of fabricated realities and incorporeal life-forms in the fog.

* * *

They tumble back into their own reality dazed and confused, their bodies tired and worn after the hours they have laid unconscious on the ground of the unnamed planet. But John can’t forget about the scent of the men he’d served with, once long ago and now dead, how they had all changed into the scent of Rodney, and how it had felt like the hands had all belonged to one person – everything is fuzzy and vague and yet sharply clear like ice.

“I’m _starving_ ,” Rodney mutters as he comes to his feet.

John remains lying for a moment longer, feeling creeping back into his extremities. He begins to move once the gate whooshes into life to bring them back home. Back to Atlantis.

* * *

Beckett calls for him to come to the doctor’s office shortly thereafter, John’s pulse still staggering as he remembers what had happened on not-Earth, his emotions spiking. He takes another pill before he goes. Must’ve been too many hours since his last one. Yes, that must be it, he tells himself; the longing had just been part of the illusions.

“Major.”

“Doc. I know what you’re going to say and I think you know my answer.”

“I am just thinking about your health, John,” Carson says. “How long do you plan to keep this up?”

“I…I don’t know.” (Forever?)

* * *

In an attempt of distraction, he follows Teyla to the mainland two days later, bringing some new supplies and medicines for them, things they cannot make on their own. She’s insightful, as always, noticing his subdued manner and John tries cracking a joke to ease up the atmosphere but thinks he’s just failing horribly. (He can’t stop thinking.)

The storm is twelve hours away.

“John, is anything the matter?” she asks, settling into the co-pilot seat.

“No, why would there be?”

The lie is so familiar and slips off his tongue with ridiculous ease, but Teyla has this way of seeing right through untrue words and John avoids looking into her eyes.

* * *

When the storm is three hours away, Atlantis has been mostly evacuated along with the people of the mainland – Ford’s jumper forced to stay and ride out the storm there - and John is rushing toward the last grounding station when an unfamiliar voice suddenly crackles in his radio. Coming to an abrupt halt, he holds his breath and listens.

_“… where is Major Sheppard?”_

He’s never heard the voice before and while Elizabeth responds calmly, he’s not quite sure she is - or that Rodney is.

They’re being held hostage by the Genii. John’s fists clenches around his rifle in anger. He doesn’t care what they want, or even who they are, it doesn’t matter; as long as his people are in danger he won’t meet their demands. He’s going to free them one way or another and defeat those who have invaded Atlantis, killing two marines in the process.

He won’t let this happen in his city.

Acustus Kolya, the man leading the Genii strike force calls himself, and even his _name_ reeks.

Jumper two is still stuck on the mainland in the clutches of the storm so for the moment he is on his own. A direct assault on the gate room is out of the question; he has no idea of the size of the strike team or of its fire-power, and he cannot risk Rodney and Elizabeth being caught in the crossfire.

But has the city on his side. One advantage is better than none.

_Hold on, Rodney. Hold on. I’ll get us out of this mess._

* * *

“Is that all?” Rodney asks stoically, glaring at their captor with icy eyes.

“No. Where is Major Sheppard?”

And Rodney’s ready to punch the man right in the face because he’ll be _damned_ if he lets this bastard lay claim on not only Atlantis but also on John. He won’t get to John, not _ever_.

He remains quiet under Kolya’s burning demands, Elizabeth avoiding the questions with ones of her own.

“How do we know you won’t kill us once we give you what you need?”

The answer is so terrifyingly simple. “You don’t.”

* * *

Suddenly Rodney’s voice fills the corridor he’s running down, out of the jumper bay.

_“…just need the C4, some medical supplies and the Wraith data device, then let them have it so they may be on their way. None of that is worth dying for.”_

At least Rodney is well enough to talk and think. That’s good. That’s good.

John’s belly keeps tying itself into knots anyway.

* * *

The radio crackles again. This time because he left one for them to find in the now empty C4 storage boxes in the armoury.

_“This is commander Kolya.”_

“Kolya? That’s difficult to pronounce. That’s a first name or a last name?” He pauses, but the man doesn’t reply. “I have hidden the C4 so that you’ll never find it. When I get confirmation that the prisoners have been safely released and allowed to gate off Atlantis, I’ll show you to it.”

_“Your offer is very generous, Major. However, DrMcKay recently told me that there is a plan in motion to save Atlantis rather than let it be taken by the storm.”_

_Damn it, Rodney!_

But he wouldn’t just reveal that. Or maybe, in his babble when he’s nervous. What have they done to him to make him talk? Held him at gunpoint? Beat him? Worse? Rodney’s strong, his instincts helping him survive, he’s alpha for goodness’ sake but he’s better at verbal battles than at physical ones and he’s unarmed at the moment. Without weapon he couldn’t have fought back even if he surely must’ve struggled a great deal – being a bother to his captors (and possibly himself).

 _Just hold on,_ John thinks again, a plan starting to form in his mind as Kolya speaks, heightening the demands.

_“The city will be ours or the ocean’s.”_

He heads for the grounding station.

* * *

Taking out the men is easy. They do not know their way around the city, spooked by the dark silence, but John knows these corridors by now like the back of his hand. One by one, they fall under his gunfire, but he doesn’t hear the shouts or the ringing of bullets. All he can think of is Rodney, trapped in the control room, probably freaking out while demanding explanation.

If they’ve hurt Rodney –

_“You killed two of my men.”_

“I guess we’re even!”

_“I don’t **like** even.”_

And then Kolya points a gun to Rodney’s head. John screams at him, voice broken across the radio and the rain, but they can probably see through the empty threats of him activating the self-destruct because if they had the intel to gain access the city they probably know that he can’t activate it on its own. The waves crash onto the pier and the thunder mixes with John’s heartbeat.

“Kolya! I’ll give you a ship! I’ll fly it out of here myself! Let. Them. _Go_.”

They can have all the C4 in the world, the supplies even and himself, he doesn’t fucking care as long as Rodney and Elizabeth are released and –

_“How is this for credibility: McKay is dead.”_

No words can make sense to the fury, the hatred coursing through his veins and everything’s so fucking screwed up and, god, god, _Rodney_ –

“I … am going … to **kill you.** ” Breaths wheezing sharply he punctuates every word, the image of Rodney imprinted on the inside of his eyelids: another broken body, slipped away, another of the men lost in battle, another killed friend, another failed mission.

_“Stay out of my way, major, or Dr Weir will join him.”_

* * *

He doesn’t know, maybe he should feel remorse, killing all these men (another reason they don’t like omegas in the military, they’re too soft-hearted, they say, their instincts not sharp enough) but he doesn’t. Their bodies are meaningless to him and he’s killed so many times before, it’s just another stitch to add to the long seam making up the lives claimed, humans and aliens and enemies.

There’s a cold vacuum spreading from his heart.

He takes out the power in the tower just like he did the men, in indifference, without tremors. He’s got to save Elizabeth and there’s still a jumper stuck on the mainland, waiting to return. There has to be a city for them to return to.

The reinforcements arrive and he raises the gate shield before they can react. By the time he’s fled the control room, the gate has already shut down after claiming dozens of lives but there’s no time or emotion to spare for him to feel proud of the accomplishment if it is one.

 _“…There are two flaws in your plan, Major,”_ Kolya apparently feels the need to inform him. By now John is running on adrenaline alone. Once it’s settled, once the storm is atop of them, part of him might just fall apart, crumbling like old stone, his enemies drowning along with him.  _“One: you actions, which leads me to the assumption that you’d rather have the city destroyed than fall to me, are childish. Second: if and when I determine Atlantis unsalvageable, Doctors Weir and McKay become obsolete.”_

No – yes – _oh god_ \- “McKay’s alive?”

Rodney’s _alive_.

And suddenly the cavern about to collapse inside him begins to rebuild, the pillars once again being put in place and holding it up.

* * *

Rodney is wet and cold and miserable and he’s not, for once, not a hundred per cent sure if it’ll work. He’s fixed the last grounding station as best he can but there are no safe bets. A few minutes earlier, power had been restored, meaning John had given in to one of Kolya’s demands, turning the naquada generator back on. Rodney is torn between anger and relief. Relief because John is still out there alive and fighting, and anger at Kolya, at the Genii, for still keeping them here, trapped in the rain.

There’s no guarantee that Kolya won’t just kill them off once they’ve gotten the shields up and the city safe. Without him or Elizabeth as hostage, there’d be no hindrance for the Genii and the only Lantean left would be John, the only thing defending him would be his P90 and, gods, Rodney doesn’t even want to think about it.

“Look,” he shouts to Elizabeth over the clashing thunder, “if this doesn’t work –”

“It will work.”

“But in the unlikely event it doesn’t –” And he sends her a desperate stare, _Please stall them, I’m horrible at talking, and I’m sorry if I fail and if you survive and I don’t, let John know that..._ He can’t finish the thought, too terrified it might slip.

She just looks at him and nods.

* * *

Then the gate filled with light and the Genii, in panic and chaos, began to retreat under the bullets hailing down from above, dragging their two prisoners along with them.

Rodney lashes out at the nearest guard, grabbing the man’s gun with his uninjured hand in a motion so quick he surprises himself as well, and has the guard’s weapon turned on himself. Adrenaline quickens his pulse. And there he sees him – John, running out into the open, risking everything, and albeit it’s subdued Rodney can sense it, his scent, familiar and warm and, gods, John’s _alive_.

“McKay! Is the shield up?!”

Rodney isn’t even sure if it’d worked until a large wave crashes onto Atlantis, cleaving as it hits the force field and shrouding the city in a great roaring shadow.

Another two men fall down on the floor, hit in the chest.

Kolya isn’t one of them.

* * *

Then the gate shuts down and goes still, save for the storm raging outside. But for now, it’s over. They exhale as one, sinking onto the floor in exhaustion, not exchanging any words for some time. Then, Teyla helps Carson to his feet – Rodney can’t place what the doctor’s even doing here – and they leave for the jumper bay where some Athosians are huddled in jumper two, waiting for it to be over. Elizabeth looks at him once, briefly, as if knowing something that he doesn’t before rising to her feet as well, pale and shaken but otherwise unharmed.

Rodney doesn’t think – well not as much as usual, anyway, as if part of his brain is numbing away along with the cut in his arm – just walks up to John and itches to touch him, embrace him, and it’s so out of character for him that it’s frightening.

John stands there calm and quiet, but there’s fire raging in his eyes and Rodney takes a deep breath, comforted by the other’s scent and warm presence.

“You okay?”

“Yeah.”

A frown creases John’s brow. “Your arm.”

“Nothing too serious,” Rodney says but adds, when John doesn’t look too convinced at the lack of complaint, “oh well it was, it hurt like hell and really, all this blood can’t be good. Oh my god, I’m having a blood loss, aren’t I? I’m going to go into shock.”

“Let’s get Beckett look you over, shall we?”

And when John speaks, so calm and collected with that familiar drawl, it’s almost like nothing’s happened except Rodney can sense the shadows of _I almost lost you_ there.

And Rodney thinks _I almost lost you too. But now you’re here and I’m okay. We’re okay._

* * *

It is, in a way, the turning point.

For the next couple of days, Rodney isn’t sure how to move on. Because while everything’s changed, nothing has changed – an incredibly bothering paradox. They’re teammates and it’s not the first time they’ve saved each other from imminent death. But something, he senses, has changed perhaps _within_ John.

It’s like the puzzle that makes up John Sheppard just has gained a few more pieces but there is no manual to make them fit and it’s driving Rodney insane as he tries figuring it all out.

It’s the scent.

John’s scent is ordinary and simple like any beta’s. They have no need for any; really, it’s just a means of identification that they themselves can hardly use because their senses are not that attuned. But, now when concentrating on it, Rodney feels some kind of _taint_ to it. Like …

… like drugs or medicines that make one’s self hazy.

But why? Why’d he…? _Unless_ …

No. That’s ridiculous. The military loathes all stretching of the rules and it is one of those unwritten, unyielding rules that omegas don’t _do_ military. For Rodney this has never really been an issue, his care of the military in general is about a teaspoon big and the one he has for the American military is even less than that, considering all of their stupid rules, and he’s an alpha so for him it hardly matters anyway.

But _what if –_


	3. Chapter 3

Why’d he let those two with them on this trip again? All right, fair enough, Gaul is the one who discovered the ancient satellite with the long-range scanners and Elizabeth had more or less ordered his presence, but why Abrams as well? They’re just … just in the way right now and Rodney has trouble concentrating after sitting in a jumper for fifteen hours, drowned in John’s scent, the other man so close and yet so far away.

“Ease up on the controls, Rodney.”

He tries, honestly, it’s not his fault that the jumper won’t fly in a straight line but in space all motion is relative so in the end it hardly matters. Right more he’s more concerned about the possibility (risk? Chance?) of a hard-on and gods he wishes he could close the bulkhead door, getting rid of those two annoying scientists so that’d just be him and John –

He’s got it fucking _bad_.

“Don’t let go of the controls!”

“Snapping doesn’t help!”

* * *

Rodney’s looking at him again, nostrils flaring and despite all the alarms going off in his head, John can’t help the shiver of the delight working its way through his body. He tries masking it, again, using a fair dose of sarcasm and Rodney nearly snaps again. But it’s at least somewhat of a distraction.

Maybe he should be glad for the two scientists – both of them beta – sitting in the back. While they complain about motion sickness at least they create this shield so that nothing … nothing will happen between him and Rodney right now. John isn’t sure what he’d do if they hadn’t been there, if it had been just him and Rodney.

He’s got another three pills hidden away in his left boot. A constant precaution he’s made sure to have for the last few years.

There is three feet of air between them and all he can sense is the heavy, heady scent of alpha, all of it Rodney’s pungent presence, and John wonders if the effects of the suppressants are starting to wear off after these long years of regular consumption.

He’s shaken out of his thoughts by Rodney’s focus shifting slightly and one of the scientists behind them exclaims something about a faint signal.

It sounds eerie and alien.

“That’s a distress call,” Rodney murmurs then. “A _Wraith_ distress call.”

* * *

The ten thousand year old ship is half-way buried in sand. Everything is silent and dead save for the distress call and the signs of a Wraith having recently fed on one of its own, which is even freakier than Wraiths in the first place.

* * *

“That thing killed Abrams!”

“And I’m sorry about that,” Rodney says, nearly screams because John can’t be thinking about going out there _alone_ – “but just because we both made an error in judgement –”

“I don’t have time to argue about this!”

(Later, Rodney would curse again and again, as he’d hesitated even as he heard the explosions and gunshots. He should _never_ have hesitated, never should have risked it.)

* * *

“You okay?”

“Other than this, and a few cracked ribs …”

Rodney can’t get the picture out of his head: the Wraith standing over John’s limp body, hand outstretched –

_Let it go. Let it go. I’m okay. We’re okay. We’re alive._

For now they both hold onto that.

* * *

John dreams of warm strong hands on his sides, holding him steady, and a body pressed close to his own, the potent scent of aroused alpha taking over his mind.

When he wakes, sweating and shivering, he struggles to roll out of bed and onto his feet, hands unsteady as he fumbles to reach the door of the bathroom adjoined to his quarters. The doors open with a quiet hiss.

Splashing water onto his face, he looks into the mirror under the dimmed lights. His eyes gleam, and he looks tired and worn out like after a long battle. He can’t forget the shadows of touch, unreal against his skin, or the feeling of _emptiness_ inside of him, needing to be filled –

Scrambling through his pack, stored inside a closet in the wall, he finds a package of pills. He’s overdone it as of late, and he knows, and the suppressants won’t last for much longer. He’ll run out of them within the month, maybe sooner, and then …

Forcing a couple of them down his throat dry, John puts the rest away, hiding them from the world. For a moment he closes his eyes, resting his forehead against the cool surface of the mirror, hands leaning against the sink.

Maybe Carson’s right. He can’t keep this up forever.

All illusions must one day be shattered.

* * *

“You truly thought a shot to the shoulder would kill me, Major?”

“Well,” John admits, “I had my hopes up that it might have.”

Kolya stands over the hatch, weapon pointed downwards, aimed at John’s head.

“Look, I’ll help you find the ZedPM if you let my team go,” Rodney says, ignoring John’s hissed protests and _Are you crazy? We need to work together, as a team, to get out of here_ but Kolya nods.

They have little choice but to trust the man’s words, for now, surrendering themselves to his mercy. As he climbs up, Rodney glances at John a final time, a thousand words ready on his tongue but he dares to utter none, all of a sudden, unable to trust himself or his control. He just looks at John and nods, quietly promising _We’ll get out of here._

* * *

By the time they do get out, Rodney is too astounded at both gaining a ZPM and suddenly knowing that John could’ve been in Mensa and John is too relieved to be alive that they realize too late they’re being double-crossed.

They return to Atlantis empty-handed, only to find out there are three Wraith hive ships on the way, two men and a jumper lost, and they have no idea what to do.

* * *

“Two weeks. What kind of defence could we mount against that in just _two weeks_?!”

It’s not the first and definitely not the last time one of those of Rodney’s tirades begins. Somehow, each time they meet up in the mess hall or the control room, the scientist can’t stop himself from mentioning it and freak out. Because three hive ships can easily wipe out Atlantis – they don’t have enough power to get the shields up more than for a few minutes, seconds if under fire. The city will burn and sink and they will all be incinerated.

“Look, McKay, there’s still time, no need to panic just yet,” John says.

“I say we _should_ panic!” That’s Carson, and Captain Cadman gives the omega a strong pat in the back that’s meant to be soothing but it only aggravates the doctor more. This is really not the place for him to be at the moment.

The air in the conference room is tenser than usual. All sorts of plans have been presented, looked over and discarded. It all comes down to this: they don’t have enough soldiers and definitely not enough power to meet the Wraith attack head on. The shields are non-existent, the weapons system offline and there are just too many civilians on the expedition team to risk it. They have been searching for evacuation sites for five days now.

Anywhere, any place to go, to _survive._

Lists are being made, people are packing belongings and data. Priority is necessary. Civilians needs to get off the city first, the scientists, the omegas and betas, the unarmed. John shifts uncomfortably in his seat as the priority list is presented, as even Elizabeth, backed up by Sergeant Bates and Carson, agrees on how important it is to get the omegas off-world. Since their coming to Atlantis, several people have mated and while there are no pregnancies yet – such risks haven’t been taken, precautions put in place – age-old partialities are hard to let go of.

When Carson glances at him across the conference table, John just stares at the data screen on the wall, pretending to listen as Grodin talks about planets possible to relocate to.

Fuck, he doesn’t want to leave Atlantis. It’s become their _home_. They can’t just … can’t just abandon it now.

But what other choices do they have?

Atlantis is the only way back to Earth. They cannot allow the Wraith to reach Earth; cannot let them lay claim on the city.

* * *

“If you’re here to tell me that I should evac with the others – ”

“I’m not. I know you’re too stubborn for that,” Carson says, shaking his head and lowering his voice; “I’ve noticed a change in you over the last few days. Is everything all right, lad?”

The silence following the statement is enough to understand what he means. He just hopes that only Carson has picked it up because the doctor has been keeping an extra eye on him for the last couple of months.

“You don’t … don’t happen to have any more suppressants around, would you, doc?” John asks quietly, glancing around to make sure they’re alone.

“Nothing with the strength that you’ve used. Those pills weren’t part of the inventory as we left here, and the only ones I’ve had have been distributed among the officially listed omegas on this base. I’m sorry, major.”

Fuck. _Fuck_.

“Doc, please, there’s got to be _something_.”

Carson would probably have liked to protest, to refuse, but he must realize that this isn’t the time. Whether he leaves now or later, it doesn’t matter, because though they can’t fight and hope to win all military personnel is expected to linger until the last moment, until the self-destruct is set and the city left to die. It’s not the time for him to let heat claim him.

So the doctor slips him a package later that night and John discretely puts it inside the arm of his jacket, keeping it there until he reaches his quarters. Another six pills. The brand is another, more legal than the one he’s used too and the effect won’t be as strong or last. But it'll have to do.

* * *

There’s been a Wraith loose in the city for two weeks. They don’t realize, though, until they find Bates beat up and unconscious in a corridor.

Then, there’s a frenzy of activity, guns are pulled out of holsters, and the marines spread out to search for it as the clock ticks faster.

* * *

John’s senses return slowly, his body full of pins and needles. Someone kneels beside him. For a moment he thinks, he _hopes_ that it’s Rodney, but there is no warm familiar presence, not a ghost of Rodney’s scent. It’s nothing safe and he shies away.

His body, heavy and sore, won’t move.

The Wraith leers down at him and John dazedly tries to reach for his sidearm, only to find his gun is far out of reach.

It breathes heavily and John realizes then that the stunner must have done something, interfering with the medications in some way or maybe it’s just wearing off dangerously quickly. The creature _knows_. He’s not even sure if the Wraith are compelled to ponder alphas and omegas, if they’re anything like humans but he’s pretty certain they’re not.

“Some of my kind would leave your sort alive, human, to ensure that we will have a supply for our next culling,” the Wraith says, its voice rough and inhuman and John shudders, feeling ill with the implications of its words. “But I have not fed for many days, and we have a new rich feeding ground waiting for us.” 

It raises its hand, tearing open his TAC vest with the other and John braces himself.

Then suddenly the Wraith’s gone, fallen aside and he senses Teyla and Ford arriving, albeit the man is standing outside his field of vision. She kneels beside him, speaking softly. “We’ve got you, major. You’re going to be okay.”

* * *

Rodney has already left with a team in a last desperate attempt to bring an old abandoned satellite online, in order to use its weapon to destroy or at least slow down the hive ships heading for them. He hears nothing of the incident with the Wraith until he returns, forty hours later, Peter Grodin dead; and worry and fear surges up in Rodney when he’s told of what happened, how they tracked down the Wraith to a lower part of the city, where it ambushed the team of marines hunting it. How John had been leading those men, the Wraith so dangerously close to feeding on him. If he’d been there …

He’s angry too, so angry at himself.

He should’ve been there. It’s what a proper alpha _should’ve_ done. Stayed with those he cares for and protected them and, damn it, even if John’s a beta he’s not even mated to, Rodney could lay down his life for him at any moment. He’d been unable to protect him then – failed as a member of his team, failed as an alpha, failed as a friend.

It might happen now, again and again, or just this once, as the Wraith bear down on them. With his last breath Grodin had been able to take out one of the hives, but two are still on the way. It’s possibly selfish to think so, because John’s a trained commanding officer, a soldier but Rodney doesn’t want him to be there – he wants him to leave with the first evac group, not wait until the last possible moment.

John has to _live_. He must ensure it.

(An ever-going mantra in his head and heart; _John has to_ _survive_.)

* * *

The self-destruct alarm hanging over them, the Stargate unexpectedly activates, opening a wormhole from Earth.

There’s a frantic rush of _How? When?_ as the marines step into the city, heavily armed, all weaponry and conviction. Colonel Everett throws the words of Elizabeth aside far too damn easily and John clenches his teeth, torn on how to act. He knows how he _should_ act, what protocol demands, how orders are given, but every fibre in his being protests to what the colonel is saying.

That a battle-ready ship is on its way is only a small consolation. How long could they possibly hope to last? Four days?

But at the mention of a ZPM soon to reach the city, Rodney’s face gains more colour than it has in days and John thinks that maybe there is some hope. If Rodney has even the faintest belief that they’ll survive, then they might. (Unless it’s all just an illusion and they’re all very, truly screwed.)

* * *

John sits in the conference room tight-lipped and tense as Colonel Everett informs them of the plan. The less attention he gains, the better. He has to bite his tongue to keep away the smart-ass remarks threatening to cross his lips.

He doesn’t miss how the alphas are glancing at him. The medicine’s wearing off and he’s ready to bolt at any moment.

All civilians have been grounded from the meeting, which he thinks is fairy insane and stupid, because input from the scientists could save lives but the colonel refuses to listen – it took a heated debate to even allow Elizabeth, their _leader_ , to participate. The room is swarming with marines, and John feels like a sore thumb and they are starting to notice it.

Six nuclear warheads. Thousands of bullets. A naquada generator to power the chair. Men who have never seen a Wraith in real life. (Almost too bad there’s nothing but a corpse left of the Wraith they’d caught the week before, John bitterly reflects, and no trace left of the one they had captured during their first two months on the base, for them to see for real.) These men really have _no idea_ what they’re up against.

Amidst the confidence he smells fear, though. They don’t know what to expect. No simulations can come near the real thing.

As the meeting concludes, John takes his leave as quickly as possible, wishing to gain at least an hour of solitude before the tempest but of course, with his luck, he immediately runs into Rodney who’s bickering with one of the marines about generators and common sense.

At seeing him, the alpha instantly breaks off the argument leaving the marine slack-jawed and perhaps terrified (Rodney’s verbal attacks can have that effect on the inexperienced) and walks up to him before John can escape. His nerves tingle when Rodney steps close, their shoulders brushing against one another and he’s certain that Rodney notices something off with his scent by now.

“Hey, Sheppard, I –”

“What is it?” he grunts out, the words sharper than intended and Rodney narrows his eyes at him. He keeps walking, taking the safest routes he can come up with, seeking corridors where no one else is walking. But Rodney follows persistently.

“Look, if we don’t make this, I, I just wanted to say – John, wait! Stop. Stop.”

Rodney speaks his name like a plead, a prayer, bringing him to a halt. John glances at him. The alpha’s eyes are gleaming in the dim, fists clenched as if they ought to be holding something but cannot find anything to grasp but air.

“I just realized, that, if you know, we don’t make it. I just wanted to say – it’s been an honour. We’re … we’re good, right?”

John forces himself to take a steadying breath so that he won’t fall over as he takes Rodney’s hand, shaking it. There are no words he can offer back (none that he dares to utter), so he just nods jerkily. “Yeah. We’re good.”

* * *

Sensors blinded by the explosions of the mines – another failed plan – they don’t discover the ships until the Wraith are right on top of them.

* * *

“Just get the damn chair working, Rodney!”

“I _am_ working on it but if I do this wrong we’re risking an overload!”

His hands are trembling. Not because of the force of the weapon he’s wielding, his mind seeking targets overhead, but being this close to Rodney is bringing him to a breaking point. The cracks are showing.

Fuck, it’s so wrong, it’s not the time, he’s warm and ill and just want to crawl into a pathetic pile and hide from the world – heat slowly envelopes him, his body’s basic needs overriding other functions.

He’s barely aware of setting the last dart aflame with a drone, sending it crashing into the ocean. He cannot think until Rodney – aware and frantic and perhaps that is why he is leaving – runs out of the room, back to the control room, leaving John slumped on the chair with sweat beading on his forehead.

* * *

After the first wave is over, the city is dark and burning in the night, and finally the backup from Earth begins to realize that it’s not as simple as it may have seemed on paper. They’re out of warheads and have lost dozens of men, shot or beamed up into darts, and are running out of power and ideas.

As Elizabeth leaves to make a deal with the Genii to gain them an a-bomb, in a desperate attempt to survive the next wave the Wraith will send, they spread their forces thin across the city to search for and destroy the Wraith that had managed to infiltrate the base during the attack.

John’s whole body aches and burns with fever and he doesn’t know how much longer he can do this. He keeps struggling because it’s the only thing he can do, clinging to the voices rasping over the radio to have a lifeline, but he cannot focus and eventually it’s all just too much, his body and emotions on overload.

Half-way between the chair and the control room, he collapses in a corner, drawing his arms around himself with a broken groan and, oh god, he’s going into heat in the middle of battle.

* * *

“Where’s Sheppard?”

Nobody can provide a satisfying answer and Rodney curses (again) about the misfortune that they haven’t got their sensors working since the last kamikaze run the darts did, knocking out most of their primary systems.

_Come on –_

The only person nearby with a strong enough gene is Carson, so Rodney ignores his protests and drags him toward the chair.

“But I can’t fly jumpers even while I’m sitting in them, how am I supposed to do that _remotely_?” the doctor cries aghast.

Wherever John’s gone, he’s hidden – or has the city hidden _him_? – somewhere in a corridor or room they don’t pass even if the place is crawling with marines and Wraith both, and Rodney finds no traces on him on the way to the chair room except the lingering scent of _omega_ and _panic_ and _heat_.

* * *

Nothing could possibly get worse than this.

Except he misses Rodney so fucking much, where he’s lying alone in the dark, wishing he’d gotten a chance to be touched by him at least _once_ but Rodney has gone to finish building an atomic bomb so that they may take out at least one of the hive ships. Just – _Rodney_ – and the Wraith are nearing the city again, far-off there’s the shrill echo of darts approaching, and vaguely he hears his radio crackling, voices asking for his position but he can’t reply.

_“Sheppard? Major Sheppard, do you copy?”_

_Oh gods Rodney. Just once. Just._

He ruts helplessly against his hand, trying to shut out the primal _need,_ to focus on the moment. There’s a battle out there. He needs to get back up there, weapon in hand, to fight. If the plan fails, if the jumper with the bomb won’t take off as it should then –

_“Sheppard? … Sheppard, this is McKay, please respond.”_

“R…’ney?” Breathe. Breathe. He can’t be still but struggles to stand.

_“Where the hell are you?! Get to the chair, Carson can’t seem to make the jumper lift and I need you here to … Sheppard, can you hear me? Sheppard!”_

He wonders if it’s a private frequency or if everyone can hear. “I’m … here.”

The jumper … they have to get it into the air. That is the whole plan. To remote control it and bring a nuke straight into one of the hives. To save Atlantis. To save home. To save Rodney. John gasps as he grabs an outcropping on the wall and pulls himself up. He’s got to – he has to (save him) – _Rodney_ –

* * *

Rodney’s cry echoes after him down the hallway.

“John! What the hell are you _doing_?!”

He mustn’t turn around. Mustn’t stop himself. Otherwise they’ll all be dead.

_“Sheppard!”_

Arriving at the loaded jumper he finds Radek fiddling with one of the controls, trying to make contact between it and the chair. The Czech looks at him shocked and bewildered when John pushes him out, closing the hatch before protests can be made. He collapses onto the pilot seat and everything goes on automatic from there, one of his hands on the controls, linked to his mind. He won’t answer the calls on the radio. Helpless in his own flesh, he guides the jumper – cloaking it with a distant thought – through the air, past the bombardments, toward one of the hives.

 _Rodney_ , he thinks, closing his eyes as he nears the large ship; he’s hot and cold, sweating out the fever settled in his soul. Regret fills him from the bottom of his heart, that he never told anyone, that he never told Rodney, that he never acknowledged anything between them, that he didn’t give in earlier just to experience a single mating.

_Live for me, Rodney. Please. **Survive**._

Then a voice urges him to de-cloak the jumper and confused, he obeys – he wants to live, he’s never wanted to die - and bright white suddenly surrounds him, the world dissolving two point three seconds before the nuke explodes.


	4. Chapter 4

He wakes up in an infirmary, drunk on sedatives.

_Atlantis?_

But there is not the steady hum of the city. This is someplace else. And he’s alive. Should he be?

“Oh, thank god you’re awake!”

_Rodney?_

“Carson’s had you on sedatives for the past seventeen hours, I was wondering if you’d _ever_ wake up, you know, with medicine involving more voodoo than science you can never be too sure. How’re you feeling?”

Yeah, that’s Rodney.

“‘m all right.” Whatever Carson’s given him as numbed his senses enough for him to think clearly, not the haze it was before, and the need is more like an itch than the swelling raw wound it was the hours before (seventeen hours?). He’s sore and thirsty but has no appetite to speak of, and he’s surprisingly whole for someone just caught in a nuke blast.

“We’re on the Daedalus,” the alpha goes on. It sounds like he’s chewing on a sandwich. Had his tongue not felt so heavy John would’ve cut in by now with some smart remark. “Commander Caldwell or what’s-his-name managed to beam you out just before the explosion occurred. Right now we’re headed back to Earth. Don’t worry, Atlantis is still standing – well, technically floating. The other hive was destroyed and we made a fairy impressive show, I mean, it was my idea after all so who is surprised - but, they left. The surviving Wraith. Thought we’d destroyed Atlantis using the self-destruct. So now they think that Lantea is nothing but empty ocean.”

“Ugh.” It’s too much at once and the words don’t properly register until afterwards. John focuses on Rodney’s presence instead, comforted by its cordiality.

Wait.

He’d entered heat. So why …?

Eyes suddenly open wide, he searches Rodney’s face for answers. “Um, Rodney…” He’s never been this collected or sane during a heat before. “I’m on meds…right?”

“Yeah. Painkillers and suppressant and whatnot. Carson said your body was in such stress after the battle and everything, but he’s letting you off on it slowly. It’s more of a … precaution,” and here Rodney clears his throat, “being on a ship with a majority of alphas on board after all. There was some frenzy and chaos when they beamed you on board to realize you were in heat. I heard you were kind of delirious so they put you in an isolated room. They beamed Carson on board to help as soon as they could.”

John flushes, feeling a mixture of shame and fear and embarrassment of outing himself like that, risking his career and integrity – and he’s thankful too, for Caldwell’s quick thinking. Being alone and in heat anyone could’ve just –

He shakes his head, trying not to think of it. (He’s not so sure that Rodney isn’t thinking it.)

“So, you know, a precaution,” Rodney finishes awkwardly. “You … you okay?”

“Think so. My head hurt like hell.” Damned side-effects. “Wait, you faked the city’s self-destruct? The Wraith’re gone?”

“By turning the shield into a cloak right after detonating a nuke above it. The Wraith bought it without question, turning on their heels when realizing there was nothing left to salvage.”

“Woah. Clever.”

“Actually I got the idea from you; I was at a blank and then, well, I realized I had to think _not_ like me and there’s nothing more opposite really than me other than you so …”

For the first time in days (possibly weeks) John smiles. “I’ll take that as a compliment.”

* * *

He remains bedridden, on Carson’s orders, for another five days. Now without the ZPM to boost its engines the Daedalus’ trip back to Earth is considerably slower than its trip to Pegasus, but John doesn’t complain. More time here means more time with Rodney. More time away from the generals and watchful eyes on Earth. And while the ship is filled with marines and security cameras, he’s relatively safe here.

He meets Steven Caldwell, the ship’s commander, two days after awakening. The meds still in his system, Carson deems it okay for him to be left alone with an alpha (Rodney being the uttermost proof of that even if John still itches to touch him). Besides, Caldwell – once he’s gotten over the initial shock – greets him mostly with indifference, like nothing could ever faze the man and they shake hands, nothing else. He seems like a good commander, respectable and smart, much like Elizabeth.

John is not given the full reports on the siege of Atlantis until he’s let out of the infirmary. They drop the bombshells then. One after the other.

* * *

First off, Colonel Everett is dead. Fed upon. They found him like a corpse in a darkened hallway, hours after the battle had ended, just barely alive and they could do nothing but ease his passing. Carson murmurs that the man’s last words were of regret and understanding, of fear of having been trapped there alone without knowing really what monsters the Wraith were. John sighs but does not grieve his death like he does for many others of the men and women who have died over the last four days. John’s glad he was aboard the Deadalus, confined to bed, during the military funeral.

* * *

There’s more (there’s always more).

Ford’s gone. Left. Addicted to the Wraith enzyme, he took off and nobody knows where. Regret courses through John that he wasn’t there to stop it from happening. That he wasn’t there to save Ford from that horrible fate. He should have been there, fulfilling his duty as team leader and yet –

“It’s not your fault, you know,” Rodney mutters when John buries his face in his hands. “He was crazy. He threatened Carson and took out two marines when stealing a jumper – they’re fine now, nothing deadly, just bruises. But he’s not sane.”

“Can we track him?”

“Maybe. Possibly. Probably not. We have no idea which address he dialled to and chances are he just, moved on, took off through the gate as soon as he was through – there’s no way of knowing.”

At least he was alive. There’s a tiny sliver of hope still.

“And you, McKay? Are _you_ all right?”

The question seems to startle Rodney. “Oh, of course. Well, considering I was nearly shot at (Teyla saved me) then almost fed on (saved by Teyla … again) and lastly nearly incinerated by an a-bomb, I’m pretty good.”

“Good. That’s good.” _I’m glad._

And John takes his hand then, on impulse. It feels more right than any action has felt for days, weeks, and Rodney strokes his knuckles with his thumb, slowly, without comment.

* * *

Half-way to the Milky Way Rodney comes to a horrible realization, now that the storm’s settled and he once again is allowed to sit down and _think_.

“They can’t send you back to Earth permanently, can they, for basically sneaking into the military?” – “There was no sneaking involved, Rodney, I just did what I had to,” John rolls his eyes at him but the scientist goes on nonetheless - “Could they court martial you? They could do that. Oh my god. They could. They _can_. Oh god! What if they send you back?!”

John winces. “Rodney …”

“We should mate. You and me. Like, now, as soon as possible. Then they can’t separate you from me, I mean us, from Atlantis, they can’t send you back then, because mates cannot be separated, even in America they’ve got to have some law or Human Rights Act concerning that.” Rodney’s babbling now, barely giving John time to get a word in edgewise. “I’ll radio General Landry as soon as we're in range that –”

“ _Rodney_!”

The alpha stills.

“Rodney,” John says again, softer this time and a small smile tugs at the corner of his lips. “Calm down.”

And he grabs Rodney’s collar, the first button of his shirt opened, and tugs him down feeling the edge of the computer resting in the man’s lap (he’s been frantically typing away the last half hour) bump against his thigh, and kisses him. It’s hot and wet and fuck, he’s needed this for _months_.

“Huh,” Rodney mutters once they part.

He frowns slightly suspiciously. “What d’you mean, ‘huh’?”

“Usually it’s the other way around. Especially the first kiss. Who initiates it, I mean. Not that I believe in all the biases.”

John glowers at him, arms crossed but he’s not _really_ angry or annoyed. It’s more the principle of the thing. “If you think you’ve gotten yourself a submissive omega that’ll kiss your feet and worship the ground you walk on, you’re entirely on the wrong continent (and possibly in the wrong galaxy).”

“Oh that’s fine,” Rodney responds, “otherwise it’d just gotten too boring anyway.”

And that’s quite all right with John, as he leans up to claim another kiss. (If not for the nurses and the security cameras …)

* * *

Earth. It’s been so many months. Coming back is off-putting and relieving and frightening all at once, because he’s not sure if it’s right to call it _home_ anymore.

“Ready?” Rodney murmurs as Deadalus settles into orbit around the planet and the senior staff of the Atlantis expedition is gathered to be beamed down to the SGC.

 _Not sure, but you’re with me so maybe_ , John thinks but nods. “Yeah.”

No hand is offered for him to grasp. He understands why (but something inside his chest twinges nonetheless).

The breath-taking view over Earth is then replaced by the grey interiors of the base within the mountain complex in Colorado. (Lieutenant) General O’Neill and (Major) General Landry are there waiting for them, along with a linguist – Doctor Daniel Jackson, if he remembers properly – whom John saw briefly in Antarctica and has read about in the SG-1 reports when killing time on the long ride back to the human homeworld.

* * *

To his great shock he isn’t fired or burned over a spit or shipped off the base to be handed over to some alpha he’s never met.

He must look quite dumb, he realizes, slack-jawed and all that when, a couple of hours later, they replace the _major_ with _lieutenant colonel_. In the background Rodney smirks, looking so smug and accomplished and proud that John can’t help himself flashing a smile back at him (okay, who did Rodney grill in order to let _this_ happen?) and for a brief moment there is nothing but the two of them.

 _I didn’t take Rodney up on his offer,_ John realizes once the ceremonies are over and he’s not been kicked out of the military or off the Atlantis project, even if people are looking at him oddly, the omega in uniform and worn boots.

Nobody dares to corner him, to push him against the wall. If they try, John’s hand twitches just so that they can see his fingers nearing the holster on his thigh and they realize that trying to claim him is just more trouble than it’s worth.

* * *

They’ve been stuck on Earth for roughly eight days and fifteen hours when Rodney suddenly bursts into John’s quarters, and John tenses for a millisecond before relaxing again, relieved that there’s no emergency or need to salute to some general he barely knows.

The astrophysicist looks as if he’s just won a Nobel. “We’re going back to Pegasus!”

Apparently, the IOA thinks the best course of action is to let the expedition team remain there and battle the Wraith a safe distance from Earth (and who would have guessed). The men and women in suits probably haven’t grasped the situation at all. They won’t, unless the hives swarm over the Earth one day and the darts crisscross over the surface of the planet, and John’s never going to let that happen.

“Thank god _, finally!_ ”

He’s getting tired of paperwork and being glanced at in the hallways, and he misses the hum of the city and Teyla’s company and the stars at night. His team isn’t whole now. They’ve got to search for Ford, and the Wraith are still out there, waiting. So much to do, so many dangers, and yet he’d choose Pegasus over Earth any day. As long as Rodney’s there beside him, it’s all going to be fine.

“John, I was thinking –”

John smirks, “Whenever aren’t you?”

“Shut up. I’ve had a chat with General Hammond. He doesn’t dislike me as much as O’Neill so it was the easiest choice and, well, the point is, if we want to mate we’ve got a go, from the military and everyone. They won’t take you away if we do, won’t force you to leave Atlantis. I mean. If you still want to. With me.” And Rodney looks so adorably nervous and fidgety that John decides to take pity on him before he hurts himself.

Honestly. John rolls his eyes. “And you’re supposed to be the genius of two galaxies.”

“So – that is a yes? Gods, _please,_ John let it be a yes-”

He smirks then.

“Patience, McKay. My next heat isn’t for another month, possibly more.” The meds have thrown his heats totally off the circles, and he’s talked with Carson about it; it’ll be awhile before the cycles will be wholly predictable again. But that’s fine. They have a city to rebuild, lives to settle back down in, hundreds of left planets to visit.

“I think I can handle the wait.”

They’re going home.

* * *

 **Home** /həʊm/  
[noun]  
 _a place for living;_  
 _a place where something began and flourished;_  
 _a place to belong_


End file.
